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Fixed crashing on alignment files without sequence data #113

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Fixed crashing on alignment files without sequence data #113

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197cbc0
Switched pysam.Samfile to pysam.AlignmentFile
Sep 20, 2017
251f3b2
Fixed bug: miso --run crashed on bam_read.seq==None
Sep 20, 2017
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2 changes: 1 addition & 1 deletion misopy/pe_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -280,7 +280,7 @@ def compute_insert_len(bams_to_process,
raise Exception, "Error: Insert length computation failed."

# Load mapped BAM filename
mapped_bam = pysam.Samfile(mapped_bam_filename, "rb")
mapped_bam = pysam.AlignmentFile(mapped_bam_filename, "rb")
###
### TODO: Rewrite this so that you only pair reads within an interval
###
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6 changes: 3 additions & 3 deletions misopy/run_events_analysis.py
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Expand Up @@ -92,14 +92,14 @@ def check_gff_and_bam(gff_dir, bam_filename, main_logger,
%(bam_index_fname))
main_logger.warning("Are you sure your BAM file is indexed?")
print "Checking if BAM has mixed read lengths..."
bam_file = pysam.Samfile(bam_filename, "rb")
bam_file = pysam.AlignmentFile(bam_filename, "rb")
n = 0
seq_lens = {}
for bam_read in bam_file:
# Check more of the reads for mixed read lengths
if n >= (num_reads * 10):
break
seq_lens[len(bam_read.seq)] = True
seq_lens[bam_read.query_alignment_length] = True
n += 1
all_seq_lens = seq_lens.keys()
if len(all_seq_lens) > 1:
Expand Down Expand Up @@ -152,7 +152,7 @@ def check_gff_and_bam(gff_dir, bam_filename, main_logger,
gff_starts_with_chr = True
n += 1
# Read first few BAM reads chromosomes
bam_file = pysam.Samfile(bam_filename, "rb")
bam_file = pysam.AlignmentFile(bam_filename, "rb")
bam_chroms = {}
bam_starts_with_chr = False
n = 0
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2 changes: 1 addition & 1 deletion misopy/sam_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,7 @@ def load_bam_reads(bam_filename,
"""
print "Loading BAM filename from: %s" %(bam_filename)
bam_filename = os.path.abspath(os.path.expanduser(bam_filename))
bamfile = pysam.Samfile(bam_filename, "rb",
bamfile = pysam.AlignmentFile(bam_filename, "rb",
template=template)
return bamfile

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2 changes: 1 addition & 1 deletion misopy/sashimi_plot/plot_utils/plot_gene.py
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Expand Up @@ -45,7 +45,7 @@ def plot_density_single(settings, sample_label,
Plot MISO events using BAM files and posterior distribution files.
TODO: If comparison files are available, plot Bayes factors too.
"""
bamfile = pysam.Samfile(bam_filename, 'rb')
bamfile = pysam.AlignmentFile(bam_filename, 'rb')
try:
subset_reads = bamfile.fetch(reference=chrom, start=tx_start,end=tx_end)
except ValueError as e:
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